RNA interference in mammals: Behind the screen

Briefings in Functional Genomics

Volumn 10, Issue 4, 2011, Pages 215-226

  Campeau, Eric ^a   Gobeil, Stéphane ^a,b  

^a UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

^b UNIVERSITÉ LAVAL   (Canada)

Author keywords

Esirna; Lentivirus; Retrovirus; Rnai screen; Shrna; Sirna

Indexed keywords

DOUBLE STRANDED RNA; MICRORNA; SHORT HAIRPIN RNA; SMALL INTERFERING RNA;

APOPTOSIS; ARTICLE; BIOLOGY; CELL VIABILITY; FUNCTIONAL PROTEOMICS; GENE EXPRESSION; GENE LIBRARY; GENE MUTATION; GENE SEQUENCE; GENETIC SCREENING; GENETIC TRANSFECTION; GENOME; HELA CELL; IN VIVO STUDY; MAMMAL; MAMMAL CELL; MICROARRAY ANALYSIS; MICROSCOPY; NONHUMAN; PHENOTYPE; RNA INTERFERENCE; VALIDATION STUDY;

ANIMALS; GENETIC TESTING; HUMANS; MAMMALS; PILOT PROJECTS; REPRODUCIBILITY OF RESULTS; RNA INTERFERENCE;

ANIMALIA; LENTIVIRUS; MAMMALIA;

EID: 80051866149     PISSN: 20412649     EISSN: 20412657     Source Type: Journal    
DOI: 10.1093/bfgp/elr018     Document Type: Article

References (95)

1. Mullenders J, Bernards R. Loss-of-function genetic screens as a tool to improve the diagnosis and treatment of cancer. Oncogene 2009;28:4409-20.
2. Hirsch AJ. The use of RNAi-based screens to identify host proteins involved in viral replication. Future Microbiol 2010; 5:303-11.
3. Wolters NM, MacKeigan JP. From sequence to function: using RNAi to elucidate mechanisms of human disease. Cell Death Differ 2008;15:809-19.
4. Mohr S, Bakal C, Perrimon N. Genomic screeningwithRNAi: results and challenges. Annu Rev Biochem 2010;79:37-64.
5. Mattila J, Puig O. Insights to transcriptional networks by using high throughput RNAi strategies. Brief Funct Genomics 2010;9:43-52.
6. Boutros M, Ahringer J. The art and design of genetic screens: RNA interference. Nat Rev Genet 2008;9:554-66.
7. Lord CJ, Martin SA, Ashworth A. RNA interference screening demystified. JClin Pathol 2009;62:195-200.
8. Zhang XD, Espeseth AS, Johnson EN, et al. Integrating experimental and analytic approaches to improve data quality in genome-wide RNAi screens. J Biomol Screen 2008;13: 378-89.
9. Falschlehner C, Steinbrink S, Erdmann G, et al. Highthroughput RNAi screening to dissect cellular pathways: a how-to guide. Biotechnol J 2010;5:368-76.
10. Sharma S, Rao A. RNAi screening: tips and techniques. Nat Immunol 2009;10:799-804.
11. Elbashir SM, Harborth J, Lendeckel W, et al. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 2001;411:494-8.
12. Yang D, Buchholz F, Huang Z, et al. Short RNA duplexes produced by hydrolysis with Escherichia coli RNase III mediate effective RNA interference in mammalian cells. Proc Natl Acad Sci USA 2002;99:9942-7.
13. Brummelkamp TR, Bernards R, Agami R. A system for stable expression of short interfering RNAs in mammalian cells. Science 2002;296:550-3.
14. McManus MT, Petersen CP, Haines BB, et al. Gene silencing using micro-RNA designed hairpins. RNA 2002;8:842-50.
15. Paddison PJ, Caudy AA, Bernstein E, et al. Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells. Genes Dev 2002;16:948-58.
16. Silva JM, Li MZ, Chang K, et al. Second-generation shRNA libraries covering the mouse and human genomes. Nat Genet 2005;37:1281-8.
17. Kittler R, Buchholz F. Functional genomic analysis of cell division by endoribonuclease-prepared siRNAs. Cell Cycle 2005;4:564-7.
18. Gopalakrishnan B, Wolff J. siRNA and DNA transfer to cultured cells. Methods Mol Biol 2009;480:31-52.
19. Fabrizio dAdf, Marzia F, Raffaella DM. Oligofection of small interfering RNAs in senescent human fibroblasts. Nat Protoc (Protoc Exch) 2006. doi:10.1038/nprot.2006.365.
20. Theis M, Buchholz F. High-throughput RNAi screening in mammalian cells with esiRNAs. Methods 2011;53:424-9.
21. Gaglione M, Messere A. Recent progress in chemically modified siRNAs. Mini Rev Med Chem 2010;10:578-95.
22. Krol J, Loedige I, Filipowicz W. The widespread regulation of microRNA biogenesis, function and decay. Nat Rev Genet 2010;11:597-610.
23. Zhang C. Novel functions for small RNA molecules. Curr Opin Mol Ther 2009;11:641-51.
24. Taft RJ, Pang KC, Mercer TR, et al. Non-coding RNAs: regulators of disease. J Pathol 2010;220:126-39.
25. Moffat J, Grueneberg DA, Yang X, et al. A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell 2006;124:1283-98.
26. Gazin C, Wajapeyee N, Gobeil S, et al. An elaborate pathway required for Ras-mediated epigenetic silencing. Nature 2007;449:1073-7.
27. Smolen GA, Zhang J, Zubrowski MJ, et al. A genome-wide RNAi screen identifies multiple RSK-dependent regulators of cell migration. Genes Dev 2010;24:2654-65.
28. Sheng Z, Li L, Zhu LJ, et al. A genome-wide RNA interference screen reveals an essential CREB3L2-ATF5-MCL1 survival pathway in malignant glioma with therapeutic implications. Nat Med 2010;16:671-7.
29. Mullenders J, Fabius AW, Madiredjo M, et al. A large scale shRNA barcode screen identifies the circadian clock component ARNTL as putative regulator of the p53 tumor suppressor pathway. PLoS One 2009;4:e4798.
30. Coussens M, Davy P, Brown L, et al. RNAi screen for telomerase reverse transcriptase transcriptional regulators identifies HIF1alpha as critical for telomerase function in murine embryonic stem cells. Proc Natl Acad Sci USA 2010; 107:13842-7.
31. Popov N, Wanzel M, Madiredjo M, et al. The ubiquitinspecific protease USP28 is required for MYC stability. Nat Cell Biol 2007;9:765-74.
32. Gumireddy K, Li A, Gimotty PA, et al. KLF17 is a negative regulator of epithelial-mesenchymal transition and metastasis in breast cancer. Nat Cell Biol 2009;11:1297-304.
33. Bric A, Miething C, Bialucha CU, et al. Functional identification of tumor-suppressor genes through an in vivo RNA interference screen in a mouse lymphoma model. Cancer Cell 2009;16:324-35.
34. Meacham CE, Ho EE, Dubrovsky E, et al. In vivo RNAi screening identifies regulators of actin dynamics as key determinants of lymphoma progression. Nat Genet 2009;41: 1133-18.
35. Zender L, Xue W, Zuber J, et al. An oncogenomics-based in vivo RNAi screen identifies tumor suppressors in liver cancer. Cell 2008;135:852-64.
36. Boettcher M, Hoheisel JD. Pooled RNAi Screens - technical and biological aspects. Curr Genomics 2010;11:162-7.
37. Boettcher M, Fredebohm J, Moghaddas Gholami A, et al. Decoding pooled RNAi screens by means of barcode tiling arrays. BMCGenomics 2010;11:7.
38. Ngo VN, Davis RE, Lamy L, etal. A loss-of-function RNA interference screen for molecular targets in cancer. Nature 2006;441:106-10.
39. Schlabach MR, Luo J, Solimini NL, et al. Cancer proliferation gene discovery through functional genomics. Science 2008;319:620-4.
40. Hartwell LH, Szankasi P, Roberts CJ, et al. Integrating genetic approaches into the discovery of anticancer drugs. Science 1997;278:1064-8.
41. Luo J, Emanuele MJ, Li D, et al. A genome-wide RNAi screen identifies multiple synthetic lethal interactions with the Ras oncogene. Cell 2009;137:835-48.
42. Scholl C, Frohling S, Dunn IF, et al. Synthetic lethal interaction between oncogenic KRAS dependency and STK33 suppression in human cancer cells. Cell 2009;137: 821-34.
43. Lam LT, Davis RE, Ngo VN, et al. Compensatory IKKalpha activation of classical NF-kappaB signaling during IKKbeta inhibition identified by an RNA interference sensitization screen. Proc Natl Acad Sci USA 2008;105: 20798-803.
44. Wiltshire TD, Lovejoy CA, Wang T, et al. Sensitivity to poly(ADP-ribose) polymerase (PARP) inhibition identifies ubiquitin-specific peptidase 11 (USP11) as a regulator of DNA double-strand break repair. J Biol Chem 2010;285: 14565-71.
45. Azorsa DO, Gonzales IM, Basu GD, et al. Synthetic lethal RNAi screening identifies sensitizing targets for gemcitabine therapy in pancreatic cancer. J Transl Med 2009;7:43.
46. Whitehurst AW, Bodemann BO, Cardenas J, et al. Synthetic lethal screen identification of chemosensitizer loci in cancer cells. Nature 2007;446:815-9.
47. O'Connell BC, Adamson B, Lydeard JR, et al. A genome-wide camptothecin sensitivity screen identifies a mammalian MMS22L-NFKBIL2 complex required for genomic stability. Mol Cell 2010;40:645-57.
48. Bukrinsky MI, Haggerty S, Dempsey MP, et al. A nuclear localization signal within HIV-1 matrix protein that governs infection of non-dividing cells. Nature 1993;365:666-9.
49. Lewis P, Hensel M, Emerman M. Human immunodeficiency virus infection of cells arrested in the cell cycle. EMBOJ 1992;11:3053-8.
50. Wajapeyee N, Serra RW, Zhu X, et al. Oncogenic BRAF induces senescence and apoptosis through pathways mediated by the secreted protein IGFBP7. Cell 2008;132: 363-74.
51. Gobeil S, Zhu X, Doillon CJ, et al. A genome-wide shRNA screen identifies GAS1 as a novel melanoma metastasis suppressor gene. Genes Dev 2008;22:2932-40.
52. Fazzio TG, Huff JT, Panning B. An RNAi screen of chromatin proteins identifies Tip60-p400 as a regulator of embryonic stem cell identity. Cell 2008;134:162-74.
53. Palakurthy RK, Wajapeyee N, Santra MK, et al. Epigenetic silencing of the RASSF1A tumor suppressor gene through HOXB3-mediated induction of DNMT3B expression. Mol Cell 2009;36:219-30.
54. Goff SP. Knockdown screens to knockout HIV-1. Cell 2008;135:417-20.
55. Brass AL, Dykxhoorn DM, Benita Y, et al. Identification of host proteins required for HIV infection through a functional genomic screen. Science 2008;319:921-6.
56. Zhou H, Xu M, Huang Q, et al. Genome-scale RNAi screen for host factors required for HIV replication. Cell Host Microbe 2008;4:495-504.
57. Konig R, Zhou Y, Elleder D, et al. Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. Cell 2008;135:49-60.
58. Neumann B, Walter T, Heriche JK, et al. Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes. Nature 2010;464:721-7.
59. Carpenter AE, Jones TR, Lamprecht MR, et al. CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol 2006;7:R100.
60. Lamprecht MR, Sabatini DM, Carpenter AE. CellProfiler: free, versatile software for automated biological image analysis. Biotechniques 2007;42:71-5.
61. Jones TR, Kang IH, Wheeler DB, et al. CellProfiler analyst: data exploration and analysis software for complex image-based screens. BMC Bioinformatics 2008;9:482.
62. Held M, Schmitz MH, Fischer B, et al. CellCognition: time-resolved phenotype annotation in high-throughput live cell imaging. NatMethods 2010;7:747-54.
63. Wild T, Horvath P, Wyler E, et al. A protein inventory of human ribosome biogenesis reveals an essential function of exportin 5 in 60 S subunit export. PLoS Biol 2010;8: e1000522.
64. Edelstein A, Amodaj N, Hoover K, et al. Computer control of microscopes using microManager. Curr Protoc Mol Biol 2010; Chapter 14:Unit14 20.
65. Conrad C, Wunsche A, Tan TH, et al. Micropilot: automation of fluorescence microscopy-based imaging for systems biology. Nat Methods 2011;8:246-9.
66. Pau G, Fuchs F, Sklyar O, et al. EBImage-an R package for image processing with applications to cellular phenotypes. Bioinformatics 2010;26:979-81.
67. Paulsen RD, Soni DV, Wollman R, et al. A genome-wide siRNA screen reveals diverse cellular processes and pathways that mediate genome stability. MolCell 2009;35:228-39.
68. Birmingham A, Selfors LM, Forster T, et al. Statistical methods for analysis of high-throughput RNA interference screens. Nat Methods 2009;6:569-75.
69. Lee S, Howell BJ. High-content screening: emerging hardware and software technologies. Methods Enzymol 2006;414: 468-83.
70. Pelz O, Gilsdorf M, Boutros M. web cellHTS2: a web-application for the analysis of high-throughput screening data. BMC Bioinformatics 2010;11:185.
71. Gilbert DF, Meinhof T, Pepperkok R, et al. DetecTiff: a novel image analysis routine for high-content screening microscopy. J Biomol Screen 2009;14:944-55.
72. Kaushal D, Naeve CW. Analyzing and visualizing expression data with Spotfire. Curr Protoc Bioinformatics 2004; Chapter 7:Unit 7 9.
73. Boutros M, Bras LP, Huber W. Analysis of cell-based RNAi screens. Genome Biol 2006;7:R66.
74. Sudbery I, Enright AJ, Fraser AG, et al. Systematic analysis of off-target effects in an RNAi screen reveals microRNAs affecting sensitivity to TRAIL-induced apoptosis. BMC Genomics 2010;11:175.
75. Cole KA, Huggins J, Laquaglia M, et al. RNAi screen of the protein kinome identifies checkpoint kinase 1 (CHK1) as a therapeutic target in neuroblastoma. Proc Natl Acad Sci USA 2011;108:3336-41.
76. Holzel M, Huang S, Koster J, et al. NF1 is a tumor suppressor in neuroblastoma that determines retinoic acid response and disease outcome. Cell 2010;142:218-29.
77. Hurov KE, Cotta-Ramusino C, Elledge SJ. A genetic screen identifies the Triple T complex required for DNA damage signaling and ATM and ATR stability. Genes Dev 2010;24:1939-50.
78. Schmitz MH, Held M, Janssens V, et al. Live-cell imaging RNAi screen identifies PP2A-B55alpha and importin-beta1 as key mitotic exit regulators in human cells. Nat Cell Biol 2010;12:886-93.
79. Smogorzewska A, Desetty R, Saito TT, et al. A genetic screen identifies FAN1, a Fanconi anemia-associated nuclease necessary for DNA interstrand crosslink repair. Mol Cell 2010;39:36-47.
80. Yoon JC, Ng A, Kim BH, et al. Wnt signaling regulates mitochondrial physiology and insulin sensitivity. Genes Dev 2010;24:1507-18.
81. Zhu YX, Tiedemann R, Shi CX, et al. RNAi screen of the druggable genome identifies modulators of proteasome inhibitor sensitivity in myeloma including CDK5. Blood 2011; 117:3847-57.
82. Ng TI, Mo H, Pilot-Matias T, et al. Identification of host genes involved in hepatitis C virus replication by small interfering RNA technology. Hepatology 2007;45:1413-21.
83. Randall G, Panis M, Cooper JD, et al. Cellular cofactors affecting hepatitis C virus infection and replication. Proc Natl Acad SciUSA 2007;104:12884-9.
84. Supekova L, Supek F, Lee J, et al. Identification of human kinases involved in hepatitis C virus replication by small interference RNA library screening. J Biol Chem 2008;283: 29-36.
85. Chia NY, Chan YS, Feng B, et al. A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Nature 2010;468:316-20.
86. Bauer JA, Ye F, Marshall CB, et al. RNA interference (RNAi) screening approach identifies agents that enhance paclitaxel activity in breast cancer cells. Breast Cancer Res 2010;12:R41.
87. Tai AW, Benita Y, Peng LF, et al. A functional genomic screen identifies cellular cofactors of hepatitis C virus replication. Cell Host Microbe 2009;5:298-307.
88. Castanotto D, Sakurai K, Lingeman R, et al. Combinatorial delivery of small interfering RNAs reduces RNAi efficacy by selective incorporation into RISC. Nucleic Acids Res 2007;35:5154-64.
89. Khan AA, Betel D, Miller ML, et al. Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs. Nat Biotechnol 2009;27:549-55.
90. Grimm D, Streetz KL, Jopling CL, et al. Fatality in mice due to oversaturation of cellular microRNA/short hairpin RNA pathways. Nature 2006;441:537-41.
91. Collinet C, Stoter M, Bradshaw CR, et al. Systems survey of endocytosis by multiparametric image analysis. Nature 2010; 464:243-9.
92. Consortium GO. Creating the gene ontology resource: design and implementation. Genome Res 2001;11:1425-33.
93. Rhodes DR, Yu J, Shanker K, et al. ONCOMINE: a cancer microarray database and integrated data-mining platform. Neoplasia 2004;6:1-6.
94. Brazma A, Hingamp P, Quackenbush J, et al. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 2001;29: 365-71.
95. Haney SA. Increasing the robustness and validity of RNAi screens. Pharmacogenomics 2007;8:1037-49.